rs118154869 (Y_RNA): Multi-tissue eQTL variant
Key takeaways
- rs118154869 sits at a Y_RNA locus, a class of small non-coding RNA genes, and influences expression of five nearby genes across multiple body tissues
- The alternate allele is linked to reduced expression in brain regions, lung, spleen, and heart, with the strongest signal in lung (SMG1P5, p=6e-7)
- MIR762HG shows increased expression in skeletal muscle, the only gene with a positive expression effect associated with the alternate allele
- No direct disease associations or metabolite connections are reported for this variant in the available data; evidence is limited to gene expression
- All expression effects are from population tissue data (GTEx v11, 953 donors) and meet a false discovery rate below 5%
Key takeaways
- rs118154869 sits at a Y_RNA locus, a class of small non-coding RNA genes, and influences expression of five nearby genes across multiple body tissues
- The alternate allele is linked to reduced expression in brain regions, lung, spleen, and heart, with the strongest signal in lung (SMG1P5, p=6e-7)
- MIR762HG shows increased expression in skeletal muscle, the only gene with a positive expression effect associated with the alternate allele
- No direct disease associations or metabolite connections are reported for this variant in the available data; evidence is limited to gene expression
- All expression effects are from population tissue data (GTEx v11, 953 donors) and meet a false discovery rate below 5%
What the research says A large metabolomics genome-wide association study examining 913 plasma metabolites in up to 19,994 individuals was conducted to map how genetic variants shape human biochemical individuality, identifying 2,599 conditionally independent variant-metabolite associations across 330 genomic regions. Separately, tissue-level expression data show that rs118154869 functions as a cis-expression quantitative trait locus (eQTL) - a variant that influences how much a nearby gene is expressed in a given tissue - for five genes across brain, lung, spleen, heart, and skeletal muscle, with all effects meeting a false discovery rate below 5% GTEx Portal.
Reported associations
- Gene expression - ENSG00000291047 (spleen and lung): The alternate allele is associated with reduced expression of this unannotated RNA gene in spleen and lung GTEx Portal
- Gene expression - SMG1P5 (brain and lung): The alternate allele is associated with reduced expression of SMG1P5 in frontal cortex (Brodmann area 9), caudate basal ganglia, and lung GTEx Portal
- Gene expression - SULT1A3 (spleen): The alternate allele is associated with reduced expression of SULT1A3, a sulfotransferase enzyme, in spleen GTEx Portal
- Gene expression - MIR762HG (skeletal muscle): The alternate allele is associated with increased expression of MIR762HG, a long non-coding RNA host gene, in skeletal muscle GTEx Portal
- Gene expression - SLX1A (heart left ventricle): The alternate allele is associated with reduced expression of SLX1A in the heart's left ventricle GTEx Portal
Evidence quality All expression associations come from GTEx v11 data (953 donors), with effects restricted to the cis-window around the variant and all meeting a false discovery rate below 5%. P-values range from approximately 9.6e-5 (SLX1A in heart left ventricle) to 6.3e-7 (SMG1P5 in lung), indicating moderate to strong statistical support for these eQTL effects GTEx Portal. Specific metabolite associations for this variant are not reported in the provided study text. No replication studies, disease endpoint analyses, or clinical outcome data are available in the provided literature, so evidence is preliminary and mechanistic only.
Tissue-specific expression effects
- ENSG00000291047: Reduced expression in spleen and lung in carriers of the alternate allele GTEx Portal
- SMG1P5: Reduced expression in frontal cortex (Brodmann area 9), caudate basal ganglia, and lung GTEx Portal
- SULT1A3: Reduced expression in spleen GTEx Portal
- MIR762HG: Increased expression in skeletal muscle GTEx Portal
- SLX1A: Reduced expression in heart left ventricle GTEx Portal
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is rs118154869?
rs118154869 is a genetic variant located at a Y_RNA locus, a region that encodes small non-coding RNA molecules. Population-level expression data show it influences how nearby genes are expressed in several tissues, including brain, lung, spleen, heart, and skeletal muscle.
What genes does rs118154869 affect?
Expression data show effects on five genes: ENSG00000291047 and SULT1A3 show reduced expression in spleen, SMG1P5 shows reduced expression in brain regions and lung, SLX1A shows reduced expression in the heart's left ventricle, and MIR762HG shows increased expression in skeletal muscle.
Is rs118154869 linked to any disease?
No direct disease associations are described in the available literature for this variant. The data available describe gene expression effects in population tissue samples only, and clinical implications have not been established.
What is a Y_RNA gene?
Y RNAs are a class of small non-coding RNA molecules found in cells. They do not code for proteins and are involved in cellular housekeeping processes. Variants near Y_RNA loci can still influence the expression of neighboring protein-coding and non-coding genes.
What does eQTL mean for this variant?
An eQTL, or expression quantitative trait locus, is a genetic variant that is statistically associated with differences in how much a nearby gene is expressed in a tissue. For this variant, that means carriers of the alternate allele tend to have measurably higher or lower amounts of certain gene transcripts in specific tissues.